EnrichmentBrowser (version 2.2.2)

compile.grn.from.kegg: Compilation of a gene regulatory network from KEGG pathways

Description

To perform network-based enrichment analysis a gene regulatory network (GRN) is required. There are well-studied processes and organisms for which comprehensive and well-annotated regulatory networks are available, e.g. the RegulonDB for E. coli and Yeastract for S. cerevisiae. However, in many cases such a network is missing. A first simple workaround is to compile a network from regulations in the KEGG database.

Usage

compile.grn.from.kegg( pwys, out.file = NULL )

Arguments

pwys

Either a list of KEGGPathway objects or an absolute file path of a zip compressed archive of pathway xml files in KGML format. Alternatively, you can specify an organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’, and the pathways will be downloaded automatically.

out.file

Optional output file the gene regulatory network will be written to.

Value

if(is.null(out.file)): the gene regulatory network; else: none, as the gene regulatory network is written to file

See Also

KEGGPathway-class, parseKGML, download.kegg.pathways

Examples

    # (1) download human pathways
    #   pwys <- download.kegg.pathways("hsa")
    # (2) compile gene regulatory network
    #   grn <- compile.grn.from.kegg(pwys)
    
    pwys <- system.file("extdata/hsa_kegg_pwys.zip", package="EnrichmentBrowser")
    hsa.grn <- compile.grn.from.kegg(pwys)